Merge branch 'main' into r-pkgs-2024

.github/workflows/website.yml

@@ -12,14 +12,12 @@ jobs:
 
       - name: preping
         run: |
-          mkdir _site
-          cp -R 0* _site
           quarto render README.qmd --to=html
-          mv README.html _site/index.html
+          mv README.html index.html
 
       - uses: actions/upload-pages-artifact@v3
         with:
-          path: "_site"
+          path: "./"
 
   website:
     if: ${{ github.event_name != 'pull_request' }}

11-rpkgs-i/lab.qmd

@@ -0,0 +1,87 @@
+---
+title: "Lab 07 - R packages"
+format:
+  html:
+    embed-resources: true
+---
+
+# Learning goals
+
+- Build an R package.
+- Use Rcpp in the package.
+- Practice your GitHub skills.
+
+# Lab description
+
+Today we will write an R package that uses `Rcpp`. To do so, we will use a
+[template package](https://github.com/UofUEpiBio/egpkg) that has the following
+set up:
+
+- Has a single Rcpp function.
+
+- Uses `roxygen2`.
+
+- Uses GitHub Actions for continuous integration.
+
+The R package doesn't have any testing in place, needs a license, and doesn't
+have coverage checking.
+
+## Question 1: Make sure you can compile the package
+
+Fork the following repository [UofUEpiBio/egpkg](https://github.com/UofUEpiBio/egpkg),
+and clone it to your local computer. Once you have a copy, do the following:
+
+1. Inspect its contents and the file located at `.github/workflows`.
+
+2. Make sure you can install it using Rstudio.
+
+3. Run R CMD check using RStudio.
+
+4. RUn R CMD check using the command line (if available).
+
+If you don't fork it and instead downloaded it manually, make sure you 
+set up a GitHub repository in your account to push your changes.
+
+## Question 2: Adding a C++ function
+
+Add the `ps_match` function [we wrote on Week 5](https://github.com/UofUEpiBio/PHS7045-advanced-programming/issues/8#issuecomment-1424974938).
+The function should be named `ps_match`:
+
+1. Add the function in a separate c++ file in the `src` folder. Make sure to document
+it using `roxygen`. Once you finish that, ensure it compiles and the function
+is visible.[^reminder] (then commit and push)
+
+[^reminder]: Remember to run `roxygen2::roxygenise()`, `devtools::document()`, or Ctr + Shift + D, if using RStudio.
+
+2. Write an example with artificial data passing a random vector with ten elements
+   distributed U[0, 1]. Add the example to the documentation using the `@examples` tag. (then commit and push)
+
+3. Write a test using the `testthat` R package. The C++ function should match the results of the equivalent R function:
+
+   ```r
+    set.seed(1231)
+    x <- cbind(runif(20))
+
+    ps_matchR <- function(x) {
+
+    match_expected <- dist(x) |> as.matrix()
+    diag(match_expected) <- .Machine$integer.max
+    indices <- apply(match_expected, 1, which.min)
+
+    list(
+        match_id = as.integer(unname(indices)),
+        match_x  = x[indices]
+    )
+
+    }
+   ```
+
+(then commit and push)
+
+## Question 3: Checkout the coverage of the package (if time permits)
+
+Using the `covr` R package, checkout the coverage using the following function
+
+```r
+covr::package_coverage()
+```